DYNAMICS STUDY OF Bacillus stearothermophilus P1 LIPASE LID BY MOLECULAR DYNAMICS SIMULATION APPROACH
Lipase (E.C. 3.1.1.3) is one of the most widely used hidrolases that has a broad applications in industrial sector, especially in industrial processes involve lipid degradation and esterification reactions. In order to obtain lipase that fit with industrial requisite, it is necessary to perform stru...
Saved in:
Main Author: | |
---|---|
Format: | Theses |
Language: | Indonesia |
Subjects: | |
Online Access: | https://digilib.itb.ac.id/gdl/view/34130 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Institution: | Institut Teknologi Bandung |
Language: | Indonesia |
Summary: | Lipase (E.C. 3.1.1.3) is one of the most widely used hidrolases that has a broad applications in industrial sector, especially in industrial processes involve lipid degradation and esterification reactions. In order to obtain lipase that fit with industrial requisite, it is necessary to perform structure-function study to elucidate interactions keys related to activity and stability as the basis of lipase engineering. One of the way to elucidate key interactions of lipase is by studying the dynamics movement of lid segment of lipase, which has been known to play a crucial role in lipase activity. Lid segment performs open and close movement in the process of substrate binding. It is intriguing to know the extent of such open and close movement of the lid segment of lipase in the absence of substrate, whether or not it reach the similar final state to the condition when the substrate is present. Such study will require atomic level investigations that cannot directly be studied by experiment due to the fast movement of the lid. Molecular dynamics simulation is one of the approach that is typically applied to investigate atomic level motion of protein. In the present study, targeted molecular dynamics (TMD) method, which is a molecular dynamics technique involving external force to accelerate molecule moving to the state that similar to a specified targeted molecule, was used to study the dynamics movement of lid segment. We used the crystal structure of thermophilic lipase from Bacillus stearothermophilus P1 (PDBID: 1J3) and Staphylococcus hycus (PDBID: 2HIH) as the targeted closed and open states of the lid of lipase, respectively. Bacillus stearothermophilus P1 lipase (BSP) consists of
388 amino acid residues and has three identified helical lid segments. Lid I, II, and III of this lipase are located within residues 289-299, 176-194, and 221-235, respectively. TMD was performed in explicit water (TIP3P) solvent at the optimum catalytic temperature of 328 K. The external harmonic force with the magnitude of
0.075 kcal(mol.Å) was applied to accelerate the dynamics movement of the lid segments of BSP. The results showed that the lid segment was not able to reach the targeted structures neither from open to closed state or vice versa. The results showed that the BSP lid was not able to reach the fully open state in the opening movements simulation of the lid. The fully open state was prevented by cooperative
non bonding interactions among Phe16, Phe176, Phe180, and Phe181 formed a hydrophobic cluster at the inner part of the lid and a salt bridge formed by Asp175 and Arg179 at the outer part of the lid. Similar problem was also found on the closing lid simulation that the fully closed was prevented by sterical hindrance among Phe180 and Phe181 as well as the salt bridge between Arg241 and Asp175. Such problem was still persist even when open-closed movement was carried out repeatedly. Mutations to those residues have relieved the barrier and made the molecules was able to reach the similar state to the targeted one. These result suggested that Phe176, Phe180, Phe181, Asp175, Arg179, and Arg241 residues of BSP lipase played important role to the dynamics movements of the lid
|
---|